|Entry||Database: PDB / ID: 5urw|
|Title||Structure of the extended type VI secretion system sheath in Myxococcus xanthus|
|Descriptor||TssB, TssC, Hcp|
|Keywords||PROTEIN TRANSPORT / T6SS / type IV secretion / protein machine / secretion system / sheath / contractile|
|Specimen source||Myxococcus xanthus (strain dk 1622) / bacteria|
Myxococcus xanthus / bacteria / ミクソコッカス・キサンタス
|Method||Electron microscopy (24 Å resolution / Cell / Subtomogram averaging)|
|Authors||Chang, Y.-W. / Rettberg, L.A. / Jensen, G.J.|
|Citation||EMBO Rep., 2017, 18, 1090-1099|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 13, 2017 / Release: May 10, 2017|
Downloads & links
Mass: 18016.617 Da / Num. of mol.: 18
Source: (natural) Myxococcus xanthus (strain dk 1622) / bacteria
References: UniProt: Q1D305
Mass: 56188.469 Da / Num. of mol.: 18
Source: (natural) Myxococcus xanthus / bacteria / ミクソコッカス・キサンタス
References: UniProt: Q1D304
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: CELL / Reconstruction method: SUBTOMOGRAM AVERAGING|
|Component||Name: Type VI secretion system / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL|
|Source (natural)||Organism: Myxococcus xanthus DK 1622|
|Buffer solution||pH: 7|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE-PROPANE|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Electron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: NONE|
|3D reconstruction||Resolution: 24 Å / Resolution method: OTHER / Number of particles: 687 / Symmetry type: POINT|
|EM volume selection||Number of tomograms: 29 / Number of volumes extracted: 687|
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi